scholarly journals Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins in Sordaria fimicola

2017 ◽  
Vol 2017 ◽  
pp. 1-10
Author(s):  
Rabia Arif ◽  
Faiza Akram ◽  
Tazeen Jamil ◽  
Hamid Mukhtar ◽  
Siu Fai Lee ◽  
...  
Keyword(s):  
Amino Acids ◽  
Mating Type ◽  
Posttranslational Modifications ◽  
Type A ◽  
Genetic Variations ◽  
Whole Genome Sequence ◽  
Short Sequence ◽  
Consensus Sequences ◽  
Wild Strains ◽  
Sordaria Fimicola

Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools. Furthermore, we have also measured and walked through genomic DNA of various Sordaria strains to determine genetic diversity by genotyping the short sequence repeats (SSRs) of wild strains of S. fimicola collected from contrasting environments of two opposing slopes (harsh and xeric south facing slope and mild north facing slope) of Evolution Canyon (EC), Israel. Based on the whole genome sequence of S. macrospora, we targeted 20 genomic regions in S. fimicola which contain short sequence repeats (SSRs). Our data revealed genetic variations in strains from south facing slope and these findings assist in the hypothesis that genetic variations caused by stressful environments lead to evolution.

scholarly journals Beyond Animals and Plants: Dynamic Maternal Effects in the FungusNeurospora crassa

2015 ◽  
Author(s):  
Kolea C. K. Zimmerman ◽  
Daniel A Levitis ◽  
Anne Pringle
Keyword(s):  
Maternal Effects ◽  
Mating Type ◽  
Strong Evidence ◽  
Cell Walls ◽  
Type A ◽  
Maternal Influence ◽  
Maternal Control ◽  
Wild Strains ◽  
Species Evolution ◽  
Spore Cell

Maternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal versus paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicocomplexans, dinoflagellates, and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed to test for maternal effects across sexual reproduction in the model fungusNeurospora crassa, we measured offspring phenotypes from crosses of all possible pairs of 22 individuals. Crosses encompassed reciprocals of 11 mating-type "A" and 11 mating-type "a" wild strains. After controlling for the genetic and geographic distances between strains in any individual cross, we found strong evidence for maternal control of sporocarp production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented, and size of pigmented spores. We propose a model linking the stage-specific presence or absence of maternal effects to cellular developmental processes: effects appear to be mediated primarily through the maternal cytoplasm, and, after spore cell walls form, maternal influence on spore development is limited. Maternal effects in fungi, thus far largely ignored, are likely to shape species' evolution and ecology. The association of anisogamy and maternal effects in a fungus suggests maternal effects may also influence the biology of other anisogamous eukaryotes.

scholarly journals Inherited Differences in Crossing Over and Gene Conversion Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1573-1593
Author(s):  
Muhammad Saleem ◽  
Bernard C Lamb ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Gene Conversion ◽  
Spontaneous Mutation ◽  
Crossing Over ◽  
Natural Genetic Variation ◽  
Evolution Canyon ◽  
Wild Strains ◽  
Sordaria Fimicola ◽  
First And Second Generation ◽  
Consistent Direction

Abstract Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II.

Inherited and Environmentally Induced Differences in Mutation Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 87-99
Author(s):  
Bernard C Lamb ◽  
Muhammad Saleem ◽  
William Scott ◽  
Nina Thapa ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Spontaneous Mutation ◽  
The South ◽  
Natural Genetic Variation ◽  
The North ◽  
Ascospore Germination ◽  
Evolution Canyon ◽  
Two Generations ◽  
Wild Strains ◽  
Sordaria Fimicola

Abstract We have studied whether there is natural genetic variation for mutation frequencies, and whether any such variation is environment-related. Mutation frequencies differed significantly between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. Strains from the harsher, drier, south-facing slope had higher frequencies of new spontaneous mutations and of accumulated mutations than strains from the milder, lusher, north-facing slope. Collective total mutation frequencies over many loci for ascospore pigmentation were 2.3, 3.5 and 4.4% for three strains from the south-facing slope, and 0.9, 1.1, 1.2, 1.3 and 1.3% for five strains from the north-facing slope. Some of this between-slope difference was inherited through two generations of selfing, with average spontaneous mutation frequencies of 1.9% for south-facing slope strains and 0.8% for north-facing slope strains. The remainder was caused by different frequencies of mutations arising in the original environments. There was also significant heritable genetic variation in mutation frequencies within slopes. Similar between-slope differences were found for ascospore germination-resistance to acriflavine, with much higher frequencies in strains from the south-facing slope. Such inherited variation provides a basis for natural selection for optimum mutation rates in each environment.

scholarly journals The Carboxy-Terminal Region ofFlavobacterium johnsoniaeSprB Facilitates Its Secretion by the Type IX Secretion System and Propulsion by the Gliding Motility Machinery

2019 ◽  
Vol 201 (19) ◽  
Author(s):  
Surashree S. Kulkarni ◽  
Joseph J. Johnston ◽  
Yongtao Zhu ◽  
Zachary T. Hying ◽  
Mark J. McBride
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cell Surface ◽  
Type A ◽  
Secretion System ◽  
Gliding Motility ◽  
Foreign Protein ◽  
Type B ◽  
Content Type ◽  
Type Ix Secretion System

ABSTRACTFlavobacterium johnsoniaeSprB moves rapidly along the cell surface, resulting in gliding motility. SprB secretion requires the type IX secretion system (T9SS). Proteins secreted by the T9SS typically have conserved C-terminal domains (CTDs) belonging to the type A CTD or type B CTD family. Attachment of 70- to 100-amino-acid type A CTDs to a foreign protein allows its secretion. Type B CTDs are common but have received little attention. Secretion of the foreign protein superfolder green fluorescent protein (sfGFP) fused to regions spanning the SprB type B CTD (sfGFP-CTDSprB) was analyzed. CTDs of 218 amino acids or longer resulted in secretion of sfGFP, whereas a 149-amino-acid region did not. Some sfGFP was secreted in soluble form, whereas the rest was attached on the cell surface. Surface-attached sfGFP was rapidly propelled along the cell, suggesting productive interaction with the motility machinery. This did not result in rapid cell movement, which apparently requires additional regions of SprB. Secretion of sfGFP-CTDSprBrequired coexpression withsprF, which lies downstream ofsprB. SprF is similar in sequence toPorphyromonas gingivalisPorP. MostF. johnsoniaegenes encoding proteins with type B CTDs lie immediately upstream ofporP/sprF-like genes. sfGFP was fused to the type B CTD from one such protein (Fjoh_3952). This resulted in secretion of sfGFP only when it was coexpressed with its cognate PorP/SprF-like protein. These results highlight the need for extended regions of type B CTDs and for coexpression with the appropriate PorP/SprF-like protein for efficient secretion and cell surface localization of cargo proteins.IMPORTANCETheF. johnsoniaegliding motility adhesin SprB is delivered to the cell surface by the type IX secretion system (T9SS) and is rapidly propelled along the cell by the motility machinery. How this 6,497-amino-acid protein interacts with the secretion and motility machines is not known. Fusion of the C-terminal 218 amino acids of SprB to a foreign cargo protein resulted in its secretion, attachment to the cell surface, and rapid movement by the motility machinery. Efficient secretion of SprB required coexpression with the outer membrane protein SprF. Secreted proteins that have sequence similarity to SprB in their C-terminal regions are common in the phylumBacteroidetesand may have roles in adhesion, motility, and virulence.

Sequence of the rat factor VIII cDNA

2004 ◽  
Vol 91 (01) ◽  
pp. 38-42 ◽  
Author(s):  
Christof Geisen ◽  
Erhard Seifried ◽  
Johannes Oldenburg ◽  
Matthias Watzka
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Factor Viii ◽  
Posttranslational Modifications ◽  
Function Analysis ◽  
Amino Acid Level ◽  
Coagulation System ◽  
Cleavage Sites ◽  
Human Factor Viii ◽  
Exon 20

SummaryFactorVIII acts as an essential compound of the tenase complex of the coagulation system. Herein we report the cDNA of the rat factor VIII. The rat cDNA comprises 6777 nucleotides and encodes a protein of 2258 amino acids, 61 amino acids less than mouse and 92 amino acids less than human factor VIII. The overall identity compared to human cDNA is 61% on the cDNA and 51% on the amino acid level. In cDNA, highest levels of sequence identity can be observed in the A and C domains (ranging between 68% and 73%), whereas B domain and the small acidic regions are more divergent (34%-49%). Compared to mouse and human most sites for posttranslational modifications such as sulfatation and glycosylation as well as thrombin and protein C cleavage sites are conserved in rat. Alternative transcripts lacking exon 17 and/or comprising additional 26 bp due to alternative splicing of exon 20 were found. Furthermore, 13 polymorphisms (seven in exon 14, one in exon 20, 23, 24, and 25, two in the 3’UTR) three of which lead to an amino acid exchange could be detected. Our findings might provide new insights into the structure-function analysis of the factor VIII protein and might prove useful for future animal models addressing the function of factor VIII.

scholarly journals Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

2020 ◽  
Author(s):  
Arun Shanker ◽  
Divya Bhanu ◽  
Anjani Alluri
Keyword(s):  
Amino Acids ◽  
Binding Sites ◽  
Tertiary Structure ◽  
Vaccine Development ◽  
Homology Modelling ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Structural Protein ◽  
Ligand Interaction ◽  
Percent Identity

<p></p><p>The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and explore the possible antiviral properties of these protein ligand complexes. Any information emerging from these protein models can be used for vaccine development. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the <a>SARS-CoV-2 </a>whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible binding with ligands that exhibit antiviral properties. Our results showed that the tertiary structure of the polyprotein isolate SARS-CoV-2_HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. <a>Our results indicate that a part of the viral genome </a><a>(residues 3268 -3573 in Frame 2 with 306 amino acids) of the SARS-CoV-2 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) </a>when modelled with template 2a5i of the PDB database had 96 percent identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase. The part of the genome (residues 1568-1882 in Frame 2 with 315 amino acids) when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. The regions studied was conserved in more than 90 genomes of SARS-CoV-2. It is possible that these viral inhibiters can be used for vaccine development for the SARS-CoV-2.</p><p></p><p></p>

scholarly journals Lantibiotic Reductase LtnJ Substrate Selectivity Assessed with a Collection of Nisin Derivatives as Substrates

2015 ◽  
Vol 81 (11) ◽  
pp. 3679-3687 ◽  
Author(s):  
Dongdong Mu ◽  
Manuel Montalbán-López ◽  
Jingjing Deng ◽  
Oscar P. Kuipers
Keyword(s):  
Amino Acids ◽  
Posttranslational Modifications ◽  
Substrate Selectivity ◽  
Biosynthesis Gene Cluster ◽  
Content Type ◽  
Hydrophobic Residues ◽  
Lacticin 3147 ◽  
Biosynthesis Gene ◽  
Biosynthetic Machinery

ABSTRACTLantibiotics are potent antimicrobial peptides characterized by the presence of dehydrated amino acids, dehydroalanine and dehydrobutyrine, and (methyl)lanthionine rings. In addition to these posttranslational modifications, some lantibiotics exhibit additional modifications that usually confer increased biological activity or stability on the peptide. LtnJ is a reductase responsible for the introduction ofd-alanine in the lantibiotic lacticin 3147. The conversion ofl-serine intod-alanine requires dehydroalanine as the substrate, which is producedin vivoby the dehydration of serine by a lantibiotic dehydratase, i.e., LanB or LanM. In this work, we probe the substrate specificity of LtnJ using a system that combines the nisin modification machinery (dehydratase, cyclase, and transporter) and the stereospecific reductase LtnJ inLactococcus lactis. We also describe an improvement in the production yield of this system by inserting a putative attenuator from the nisin biosynthesis gene cluster in front of theltnJgene. In order to clarify the sequence selectivity of LtnJ, peptides composed of truncated nisin and different mutated C-terminal tails were designed and coexpressed with LtnJ and the nisin biosynthetic machinery. In these tails, serine was flanked by diverse amino acids to determine the influence of the surrounding residues in the reaction. LtnJ successfully hydrogenated peptides when hydrophobic residues (Leu, Ile, Phe, and Ala) were flanking the intermediate dehydroalanine, while those in which dehydroalanine was flanked by one or two polar residues (Ser, Thr, Glu, Lys, and Asn) or Gly were either less prone to be modified by LtnJ or not modified at all. Moreover, our results showed that dehydrobutyrine cannot serve as a substrate for LtnJ.

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